Contacts of the strand formed by residues 284 - 291 (chain A) in PDB entry 4CKG
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 284 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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273A PHE* 3.9 8.1 - - - -
274A LYS* 2.8 39.7 + - - +
282A THR 5.1 1.0 + - - -
283A TRP* 1.3 75.6 - - - +
285A ARG* 1.3 59.4 + - - +
286A ARG* 3.9 31.5 + - - +
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Residues in contact with ARG 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A GLU* 5.5 0.2 + - - -
271A HIS* 3.6 37.0 + - + +
272A LEU* 3.2 23.3 - - - +
273A PHE* 3.0 41.5 - - + -
284A SER* 1.3 75.5 - - - +
286A ARG* 1.3 78.9 + - - +
299A LYS 5.3 1.4 - - - +
343A ASP* 2.7 46.4 + - - -
135B GLU* 5.7 8.5 - - - -
138B LEU* 3.7 30.9 - - - +
139B THR* 5.9 0.4 - - - -
163B ARG* 5.8 0.8 - - - +
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Residues in contact with ARG 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A HIS* 3.4 10.4 - - - +
272A LEU 3.3 26.2 + - - -
274A LYS* 4.6 13.1 - - + +
284A SER* 3.9 28.7 + - - +
285A ARG* 1.3 84.4 + - - +
287A TRP* 1.3 59.9 + - - +
288A PHE* 3.5 19.1 - - + -
297A TYR* 3.7 37.0 - - + -
298A GLN 4.3 0.9 - - - +
299A LYS* 3.9 49.1 + - - +
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Residues in contact with TRP 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A GLU* 3.7 27.3 - - + +
270A GLY* 3.5 27.3 - - - +
271A HIS* 3.5 39.3 - + - +
286A ARG* 1.3 72.1 - - - +
288A PHE* 1.4 60.9 + - - +
289A THR* 4.8 6.4 + - - -
297A TYR* 3.3 19.1 - - - -
298A GLN* 3.3 58.2 + - + +
300A LYS 5.5 2.5 - - - +
301A TYR* 4.0 35.2 - + - -
15B PRO* 4.2 19.1 - - + -
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Residues in contact with PHE 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A GLU* 3.3 2.5 - - - +
270A GLY 3.0 36.2 + - - +
272A LEU* 3.9 34.1 - - + -
274A LYS* 3.9 21.1 - - + -
286A ARG* 3.5 29.8 - - + -
287A TRP* 1.4 73.5 - - - +
289A THR* 1.3 68.6 + - - +
295A LEU* 3.8 17.9 - - + -
296A VAL 3.3 14.8 - - - -
297A TYR* 3.9 8.5 - - + -
308A VAL* 3.6 22.2 - - + -
340A LEU* 3.7 28.0 - - + -
351A TRP* 3.7 17.5 - - + -
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Residues in contact with THR 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A VAL* 4.9 7.0 - - + -
268A MET 3.4 13.2 - - - +
269A GLU* 3.5 16.1 - - + +
287A TRP* 4.7 8.3 + - - -
288A PHE* 1.3 81.1 + - - +
290A ILE* 1.4 73.9 + - - +
291A GLN* 4.2 14.4 - - + +
294A GLN 3.3 1.6 - - - +
295A LEU* 4.4 2.7 - - - -
296A VAL* 2.8 49.8 + - + +
298A GLN* 4.9 8.1 + - - -
305A VAL* 5.2 3.4 - - - +
351A TRP* 5.0 0.2 - - - -
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Residues in contact with ILE 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A LEU* 3.0 29.9 - - + +
267A VAL* 3.5 1.9 - - - -
268A MET* 2.9 36.8 + - + +
289A THR* 1.4 70.6 - - - +
291A GLN* 1.4 62.4 + - - +
293A ASN* 4.5 4.0 - - - +
294A GLN 3.4 17.9 - - - +
295A LEU* 4.5 8.7 - - + +
312A LEU* 5.1 1.1 - - + -
351A TRP* 4.2 13.9 - - + -
354A ALA* 4.0 28.3 - - + +
355A VAL* 3.9 25.4 - - + -
358A SER* 3.6 24.0 - - - +
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Residues in contact with GLN 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A GLU* 5.1 3.8 + - - -
265A GLY 4.0 2.5 - - - -
267A VAL* 3.5 33.1 - - + +
289A THR* 3.7 14.3 + - + +
290A ILE* 1.4 74.3 - - - +
292A SER* 1.4 76.9 + - - +
293A ASN 3.3 2.0 - - - -
294A GLN* 2.9 31.1 + - - +
296A VAL* 5.9 2.7 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il